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It is four months after the Cylons occupied New Caprica and forced Galactica and Pegusus to abandon the 39,000 colonists there. The Cylons are fighting against an insurgency by recruiting a human police force of Cylon sympathisers some two hundred strong. Col. Tigh has been in a Cylon prison for an unknown length of time; he has been repeatedly tortured and lost an eye. The only thing he can do is etch a wall tally for his days in confinement, which a Number One interrogator reveals is frequently altered to confuse him. Ellen Tigh has sex with another Number One in the hopes of negotiating her husband's release, which is successful. A Number Three, the D'anna from "Downloaded", seeks an Oracle to explain strange dreams she has been having; the Oracle communicates a message from God, announcing that Hera is alive. The resistance, currently led by Samuel T. Anders and Galen Tyrol, are running a bombing campaign in New Caprica City, targeting Cylon infrastructure such as their dockyard. Lt. Thrace meanwhile has been imprisoned by a Number Two, the Leoben she met a year ago. Forced to live in an apartment with him in a pseduo-marital relationship, she has fashioned a shiv, and stabs him in the neck when the resistance's latest bomb goes off. With his dying breath, he reminds her he will come back.

President Gaius Baltar is woken up by the bombing and has been increasingly stressed by past four months of occupation. He has restarted a relationship with Caprica Six, but their relationship is slowly falling apart due to his behaviour and he does not consider her almost being boxed because of her feelings for him.

Number Three goes over to a make-shift hospital tent as Dr. Cottle's team tries to save a Number Five injured by shrapnel in the resistance bombing. She inquires about Hera's apparent death, and becomes suspicious of his behaviour, seeing it as proof of the Oracle's word. As Number Three departs, a mysterious man walks past the tent and gives a nearby dog, Jake, a treat before flipping over his dog bowl before walking away.

That night Chief Tyrol leaves Cally with the baby and goes over to the dog. He rights the dog bowl and goes into a nearby refuse yard and recovers a plastic envelope containing official documents from the President's office. Tyrol joins Anders in welcoming back Tigh from captivity. Tigh is revealed to be the resistance's leader, and asks what target Anders and Tyrol were planning next; Tyrol reveals the secret documents, which contain information on a graduation ceremony at the New Caprica Police Academy. President Baltar is due to attend, which will make him a prized target in a terror attack, though Tyrol doesn't want anyone getting hurt. Tigh disagrees; the police graduates are traitors, and they must be killed to serve as a message to sympathisers. Tigh asks about the wireless, and Tyrol explains that every day they send a wireless message out hoping to make contact with Galactica, but it is always jammed. He hopes the mystery source will give the resistance information on radio frequencies so they can make contact.

The Number Two, Leoben, returns to his apartment to greet Kara, revealing this is the fifth time he's been killed by her. Kara tries to trick him into accepting a hug, but he has her throw the shiv away. Leoben firmly believes that the two are destined to be together and wants her to accept him. He goes into the bedroom to sleep, but rather than join him Kara rushes for the door, which is locked from the other side.

Back with the fleet, things are not going well. The Cylons occupied New Caprica while Galactica and Pegasus were running skeleton crews, and they are having to train new pilots before they have any chance of rescuing the colonists. Kat has been promoted to CAG, and oversees rehearsal for the rescue plan involving decoy drones from her Viper. The rehearsal, the sixteenth, fails when a Raptor fires its drone out of sync and nearly kills Racetrack. Helo, Galactica's new XO, acknowledges Kat's abort request, but the Admiral insists they try yet again. Commander Adama, who has gained weight in the past few months from stress, confronts his father and senior officer; the pilots are tired and failing the seventeenth time is inevitable. The Admiral insists they continue the training, but it is scrubbed when two Vipers collide, possibly from pilot fatigue as they have been practising for eleven hours straight.

Back on New Caprica, Anders and Tucker "Duck" Clellan participate in a Pyramid match, and use the ball play as a means of giving insurgent instructions. Duck's wife, Nora, was killed by the Cylons and, after a meeting with Oracle Dodona, he believes he has nothing left to live for. Having infiltrated the New Caprica police, Tigh has put him on a suicide mission. Tyrol pleads with Tigh to avoid suicide missions but he will have none of it, while Anders gets an answer straight from Duck that the mission is something he wants.

On Galactica, Admiral Adama has had all he can stand with his son. Lee pleads that the two Battlestars are at half-strength and can't take on the Cylons, but William sees it as the excuses of a cowardly and self-defeatist officer and threatens to have him replaced as Pegasus' CO if he doesn't motivate his crew.

Laura Roslin converses with Anders about Hera's safety. Anders assures her she and her adoptive mother Maya are safe and, as high-profile targets, are moved around the city every two or three days. Anders understands Roslin's insistence that the Cylons can never capture the two, and he must keep them away from the very possibility of having to kill them to avoid capture. Hera, she says, is "the shape of things to come", but won't reveal her true nature to anyone, even her own security.

The Cylon leaders of the occupation hold a meeting onboard Colonial One, consisting of two Number Ones; the Number Three; two Number Fives, Caprica Six and Boomer. The Cylons had voted in favour of settling on New Caprica to help the humans recover from the Fall of the Twelve Colonies. The Number Ones, more interesting in brutality, consider having Baltar executed to put fear in the colonists. Caprica Six won't allow it, but the Ones don't care; the Number Fives save him instead by pointing out he is so hated the New Capricans would celebrate it instead. The Ones propose that, instead, the insurgent leaders are publicly executed, followed by random members of the public until resistance to the occupation ends.

Around New Caprica, Tyrol finally receives information about Cylon radio frequencies from the mystery source, which should give the resistance a means of contacting Galactica. At the apartment, meanwhile, Kara attempts to kill herself by cutting her wrist in the bathroom, which fails when Leoben finds her right after.

On Pegasus, Lee is still recovering from the berating he received. When Anastasia fails to back him up, he takes it out on her. She explains to him that his recent failings are due to the job, that he doesn't like being like his father and has instead given up on life instead. On Galactica, the Admiral sits with Sharon who, over the past sixteen months, has gained comforts such as furniture in her cell while slowly building trust with him. She believes he is consumed by guilt over leaving the 39,000 colonists behind and that it is preventing him from doing his job properly. He takes her view into consideration.

In the morning, Racetrack and Skulls sit on board a recon raptor sent on the latest daily mission to the nebula. The Cylons have caught on about the recon Raptors, and Racetrack doesn't want to stay any longer than they have to. In the last minute before they return to Galactica, Skulls picks up a wireless message from the resistance. The Raptor sends only one message to the ground before leaving: “Will make contact this freq every twelve hours. Prepare sitrep for
command authority. Have hope. We’re coming for you.”

Meanwhile, Duck puts on a suicide vest, intent on blowing himself up at the graduation ceremony and killing everyone in it. Tigh and Tyrol discuss abandoning the mission since Galactica will return shortly, but Tigh will not allow an attack on Baltar to be cancelled unless Tyrol's source confirms he isn't coming. Gaeta enters the Presidential office to inform Baltar it is time for the graduation; he decides against it due to security issues. Gaeta runs out of Colonial One and flips over Jake's bowl outside the hospital tent, revealing he is the source. D'anna walks past the hospital tent and, seeing the flipped-over dog bowl, feels the need to flip it right right way. When Tyrol checks the bowl, he mistakenly believes there is no message and Baltar is indeed at the ceremony. Duck dresses up in his uniform, ready for the graduation. As the Cylon commanders shake the hands of each graduate, he whispers, "I'll see you soon, Nora" and detonates a suicide vest, killing dozens.

Occupation and Precipice were written side-by side as a single two-hour story which could be split into two in syndication. Executive Producer Ronald D. Moore wanted the New Caprica story to be concluded in fewer than five weeks, and Occupation and Precipice were as a result aired on the same day.[1]

The first draft was completed on 1 April 2006, with the final revisions made on 3 May.